Fwd: seeking help on cghMCR pleeeease
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Hi, I sent this email a while back and didn't get any reply, could anybody help please? thanks Nathalie -------- Original Message -------- Subject: seeking help on cghMCR pleeeease Date: Mon, 12 Dec 2011 14:17:58 +0000 From: Nathalie Conte <nac@hinxton.sanger.ac.uk> To: bioconductor at r-project.org HI, I am using cghMCR and I would need some advice on the software behaviour. I don't seem to get any different results when I change the gapAllowed parameter. I have used DNAcopy to create a segmented data for all my samples. Then I choose to use cghMCR to get common alterations between my samples. These are all arguments from the package doc(latest version): segments is a data frame extracted from the "output" element of the object returned by segment of the package DNAcopy or getSegments gapAllowed is an integer specifying low threshold of base pair number to separate two adjacent segments, belower which the two segments will be joined as an altered span alteredLow is a positive number between 0 and 1 specifying the lower resh- old percential value. Only segments with values falling below this threshold are considered as altered span alteredHigh is a positive number between 0 and 1 specifying the upper resh- old percential value. Only segments with values falling over this threshold are considered as altered span recurrence is an integer between 1 and 100 that specifies the rate of occur- rence for a gain or loss that are observed across sample. Only gains/losses with ocurrence rate grater than the threshold values are declared as MCRs spanLimit is an integer that defines the leangh of altered spans that can be considered as locus. It is not of any use at this time thresholdType is a character string that can be either "quantile" or "value" indicating wether alteredLow or alteredHigh is quantial or actual value In my analysis, I have used cghMCR with threshold value log2R of low -0.25 and high =0.25 , a spanLimit of 2.10^7 and I have tried several gapAllowed values, 5, 500 , 5000 and 50000 .Each time I used the MCR function to identify the minimum regions. I have put an example of each results only on 25 lines of chromosome 4 to avoid massive sized files (see attached) , but basically whatever the gapAllowed size i get the same MCRs at the end for all postitions. I would expect this to vary as segments should be fused together differently given this parameter.. Could you please help with this and advise on what I might be doing wrong? Is spanLimit any use? in the doc, It is written "It is not of any use at this time"?? Another point, the gapAllowed is specified " is an integer specifying low threshold of base pair number " is the unit in base pair number, in several examples it seems that the units are in kb??? thanks a lot , code for gapAllowed=5 ##get the cghMCR function with these parameters cghmcr0.25T_5k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5, gapAllowed = 5, alteredLow = -0.25,alteredHigh = 0.25, spanLimit=20000000,recurrence=2,thresholdType=c("value")) ##identify the MCRs mcrs0.25T_5k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_5k_2_20M_sdundo1.5) mcrs0.25T_5k_2_20M_sdundo.bind1.5 <-cbind ( mcrs0.25T_5k_2_20M_sdundo1.5[, c ( "chromosome", "status", "loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] ) write.table(mcrs0.25T_5k_2_20M_sdundo.bind1.5, file="PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5.txt", sep="\t", row.names=F) PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_5k_ 2_20M_sdundo.bind1.5.txt", sep="\t", header=T) ##only 25 lines of chromsome 4 test.5k=head(PT_mcrs0.25T_5k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_5k_2_20 M_sdundo.bind1.5==4,],25) ##attached data write.table(test.5k, file="test.5k.txt", sep="\t") code for gapAllowed=500 cghmcr0.25T_500k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5, gapAllowed = 500, alteredLow = -0.25,alteredHigh = 0.25, spanLimit=20000000,recurrence=2,thresholdType=c("value")) mcrs0.25T_500k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_500k_2_20M_sdundo1.5) mcrs0.25T_500k_2_20M_sdundo.bind1.5 <-cbind ( mcrs0.25T_500k_2_20M_sdundo1.5[, c ( "chromosome", "status", "loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] ) write.table(mcrs0.25T_500k_2_20M_sdundo.bind1.5, file="PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5.txt", sep="\t", row.names=F) PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_5 00k_2_20M_sdundo.bind1.5.txt", sep="\t", header=T) test.500k=head(PT_mcrs0.25T_500k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_500 k_2_20M_sdundo.bind1.5==4,],25) write.table(test.500k, file="test.500k.txt", sep="\t") code for gapAllowed=5000 cghmcr0.25T_5000k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5, gapAllowed = 5000, alteredLow = -0.25,alteredHigh = 0.25, spanLimit=20000000,recurrence=2,thresholdType=c("value")) mcrs0.25T_5000k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_5000k_2_20M_sdundo1.5 ) mcrs0.25T_5000k_2_20M_sdundo.bind1.5 <-cbind ( mcrs0.25T_5000k_2_20M_sdundo1.5[, c ( "chromosome", "status", "loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] ) write.table(mcrs0.25T_5000k_2_20M_sdundo.bind1.5, file="PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5.txt", sep="\t", row.names=F) PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25T_ 5000k_2_20M_sdundo.bind1.5.txt", sep="\t", header=T) test.5000k=head(PT_mcrs0.25T_5000k_2_20M_sdundo.bind1.5[PT_mcrs0.25T_5 000k_2_20M_sdundo.bind1.5==4,],25) write.table(test.5000k, file="test.5000k.txt", sep="\t") code for gapAllowed=500000 cghmcr0.25T_500000k_2_20M_sdundo1.5 <- cghMCR(sdundo.segData_order1.5, gapAllowed = 500000, alteredLow = -0.25,alteredHigh = 0.25, spanLimit=20000000,recurrence=2,thresholdType=c("value")) mcrs0.25T_500000k_2_20M_sdundo1.5<-MCR(cghmcr0.25T_500000k_2_20M_sdund o1.5) mcrs0.25T_500000k_2_20M_sdundo.bind1.5 <-cbind ( mcrs0.25T_500000k_2_20M_sdundo1.5[, c ( "chromosome", "status", "loc.start", "loc.end","mcr.start", "mcr.end","samples" ) ],z[1:9171] ) write.table(mcrs0.25T_500000k_2_20M_sdundo.bind1.5, file="PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5.txt", sep="\t", row.names=F) PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5=read.table(file="PT_mcrs0.25 T_500000k_2_20M_sdundo.bind1.5.txt", sep="\t", header=T) test.500000k=head(PT_mcrs0.25T_500000k_2_20M_sdundo.bind1.5[PT_mcrs0.2 5T_500000k_2_20M_sdundo.bind1.5==4,],25) write.table(test.500000k, file="test.500000k.txt", sep="\t") sessioninfo() R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] cghMCR_1.10.0 limma_3.4.5 CNTools_1.6.0 genefilter_1.30.0 [5] DNAcopy_1.22.1 loaded via a namespace (and not attached): [1] annotate_1.26.1 AnnotationDbi_1.10.1 Biobase_2.8.0 [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.13.0 [7] survival_2.35-8 xtable_1.6-0 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -------------- next part -------------- "chromosome" "status" "loc.start" "loc.end" "mcr.start" "mcr.end" "samples" "X" "1236" 4 "gain" 3012291 93945684 3012291 3104649 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6 b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146 9518784.txt" 7 "1237" 4 "gain" 3012291 93945684 3104649 3271379 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h _PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1238" 4 "gain" 3012291 93945684 3271379 3335299 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1239" 4 "gain" 3012291 93945684 3335299 3353037 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1240" 4 "gain" 3012291 93945684 3353037 3804119 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1241" 4 "gain" 3012291 93945684 3804119 3810172 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1242" 4 "gain" 3012291 93945684 3810172 3825707 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1243" 4 "gain" 3012291 93945684 3825707 3882946 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt" 7 "1244" 4 "gain" 3012291 93945684 3882946 5377872 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1245" 4 "gain" 3012291 93945684 5377872 5386981 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1246" 4 "gain" 3012291 93945684 5386981 5656761 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1247" 4 "gain" 3012291 93945684 5656761 5661982 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1248" 4 "gain" 3012291 93945684 5661982 6045858 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1249" 4 "gain" 3012291 93945684 6045858 6055446 "PPAB_ 15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1250" 4 "gain" 3012291 93945684 6055446 6210181 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1251" 4 "gain" 3012291 93945684 6210181 6273347 "PPAB_ 17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1252" 4 "gain" 3012291 93945684 6273347 6649553 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1253" 4 "gain" 3012291 93945684 6649553 6655783 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_ 251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1254" 4 "gain" 3012291 93945684 6655783 6817158 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_ 251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1255" 4 "gain" 3012291 93945684 6817158 6941107 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1256" 4 "gain" 3012291 93945684 6941107 7274363 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1257" 4 "gain" 3012291 93945684 7274363 7795963 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1258" 4 "gain" 3012291 93945684 7795963 8405887 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5 "1259" 4 "gain" 3012291 93945684 8405887 8478629 "PKBL_ 11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1260" 4 "gain" 3012291 93945684 8478629 9241084 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5 -------------- next part -------------- "chromosome" "status" "loc.start" "loc.end" "mcr.start" "mcr.end" "samples" "X" "1236" 4 "gain" 3012291 93945684 3012291 3104649 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6 b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146 9518784.txt" 7 "1237" 4 "gain" 3012291 93945684 3104649 3271379 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h _PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1238" 4 "gain" 3012291 93945684 3271379 3335299 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1239" 4 "gain" 3012291 93945684 3335299 3353037 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1240" 4 "gain" 3012291 93945684 3353037 3804119 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1241" 4 "gain" 3012291 93945684 3804119 3810172 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1242" 4 "gain" 3012291 93945684 3810172 3825707 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1243" 4 "gain" 3012291 93945684 3825707 3882946 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt" 7 "1244" 4 "gain" 3012291 93945684 3882946 5377872 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1245" 4 "gain" 3012291 93945684 5377872 5386981 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1246" 4 "gain" 3012291 93945684 5386981 5656761 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1247" 4 "gain" 3012291 93945684 5656761 5661982 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1248" 4 "gain" 3012291 93945684 5661982 6045858 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1249" 4 "gain" 3012291 93945684 6045858 6055446 "PPAB_ 15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1250" 4 "gain" 3012291 93945684 6055446 6210181 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1251" 4 "gain" 3012291 93945684 6210181 6273347 "PPAB_ 17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1252" 4 "gain" 3012291 93945684 6273347 6649553 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1253" 4 "gain" 3012291 93945684 6649553 6655783 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_ 251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1254" 4 "gain" 3012291 93945684 6655783 6817158 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_ 251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1255" 4 "gain" 3012291 93945684 6817158 6941107 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1256" 4 "gain" 3012291 93945684 6941107 7274363 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1257" 4 "gain" 3012291 93945684 7274363 7795963 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1258" 4 "gain" 3012291 93945684 7795963 8405887 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5 "1259" 4 "gain" 3012291 93945684 8405887 8478629 "PKBL_ 11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1260" 4 "gain" 3012291 93945684 8478629 9241084 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5 -------------- next part -------------- "chromosome" "status" "loc.start" "loc.end" "mcr.start" "mcr.end" "samples" "X" "1236" 4 "gain" 3012291 93945684 3012291 3104649 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6 b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146 9518784.txt" 7 "1237" 4 "gain" 3012291 93945684 3104649 3271379 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h _PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1238" 4 "gain" 3012291 93945684 3271379 3335299 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1239" 4 "gain" 3012291 93945684 3335299 3353037 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1240" 4 "gain" 3012291 93945684 3353037 3804119 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1241" 4 "gain" 3012291 93945684 3804119 3810172 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1242" 4 "gain" 3012291 93945684 3810172 3825707 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1243" 4 "gain" 3012291 93945684 3825707 3882946 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt" 7 "1244" 4 "gain" 3012291 93945684 3882946 5377872 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1245" 4 "gain" 3012291 93945684 5377872 5386981 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1246" 4 "gain" 3012291 93945684 5386981 5656761 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1247" 4 "gain" 3012291 93945684 5656761 5661982 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1248" 4 "gain" 3012291 93945684 5661982 6045858 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1249" 4 "gain" 3012291 93945684 6045858 6055446 "PPAB_ 15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1250" 4 "gain" 3012291 93945684 6055446 6210181 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1251" 4 "gain" 3012291 93945684 6210181 6273347 "PPAB_ 17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1252" 4 "gain" 3012291 93945684 6273347 6649553 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1253" 4 "gain" 3012291 93945684 6649553 6655783 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_ 251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1254" 4 "gain" 3012291 93945684 6655783 6817158 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_ 251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1255" 4 "gain" 3012291 93945684 6817158 6941107 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1256" 4 "gain" 3012291 93945684 6941107 7274363 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1257" 4 "gain" 3012291 93945684 7274363 7795963 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1258" 4 "gain" 3012291 93945684 7795963 8405887 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5 "1259" 4 "gain" 3012291 93945684 8405887 8478629 "PKBL_ 11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1260" 4 "gain" 3012291 93945684 8478629 9241084 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5 -------------- next part -------------- "chromosome" "status" "loc.start" "loc.end" "mcr.start" "mcr.end" "samples" "X" "1236" 4 "gain" 3012291 155625629 3012291 3104649 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_20_8b_PT_251469518736.txt,PPAB_3_6 b_PT_251469518594.txt,PPAB_9_4h_PT_251469518768.txt,PPAC_4_1c_PT_25146 9518784.txt" 7 "1237" 4 "gain" 3012291 155625629 3104649 3271379 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_142538_PT_251469518750.txt, PPAB_15_1d_PT_251469518744.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_4h _PT_251469518768.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1238" 4 "gain" 3012291 155625629 3271379 3335299 "PKBL_ 11_2a_PT_PapillenTumor_1469518286.txt,PPAB_15_1d_PT_251469518744.txt,P PAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1239" 4 "gain" 3012291 155625629 3335299 3353037 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_3_6b_PT_251469518594.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1240" 4 "gain" 3012291 155625629 3353037 3804119 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1241" 4 "gain" 3012291 155625629 3804119 3810172 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1242" 4 "gain" 3012291 155625629 3810172 3825707 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1243" 4 "gain" 3012291 155625629 3825707 3882946 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt,PPDK_8_1a_PT_251469518785.txt" 7 "1244" 4 "gain" 3012291 155625629 3882946 5377872 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1245" 4 "gain" 3012291 155625629 5377872 5386981 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1246" 4 "gain" 3012291 155625629 5386981 5656761 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1247" 4 "gain" 3012291 155625629 5656761 5661982 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1248" 4 "gain" 3012291 155625629 5661982 6045858 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1249" 4 "gain" 3012291 155625629 6045858 6055446 "PPAB_ 15_1d_PT_251469518744.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1250" 4 "gain" 3012291 155625629 6055446 6210181 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1251" 4 "gain" 3012291 155625629 6210181 6273347 "PPAB_ 17_2b_PT_251469518522.txt,PPAB_17_2c_PT_251469518521.txt,PPAB_24_1f_PT _251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_251469518 575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 7 "1252" 4 "gain" 3012291 155625629 6273347 6649553 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1253" 4 "gain" 3012291 155625629 6649553 6655783 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_9_1g_PT_ 251469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1254" 4 "gain" 3012291 155625629 6655783 6817158 "PPAB_ 17_2c_PT_251469518521.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_4_9a_PT_ 251469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2514695187 84.txt" 5 "1255" 4 "gain" 3012291 155625629 6817158 6941107 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1256" 4 "gain" 3012291 155625629 6941107 7274363 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_2 51469518784.txt" 3 "1257" 4 "gain" 3012291 155625629 7274363 7795963 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_9_1g_PT_2 51469518604.txt,PPAC_4_1c_PT_251469518784.txt" 4 "1258" 4 "gain" 3012291 155625629 7795963 8405887 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5 "1259" 4 "gain" 3012291 155625629 8405887 8478629 "PKBL_ 11_2d_PT_251469518714.txt,PPAB_24_1f_PT_251469518532.txt,PPAB_3_6b_PT_ 251469518594.txt,PPAB_4_9a_PT_251469518575.txt,PPAB_9_1g_PT_2514695186 04.txt,PPAC_4_1c_PT_251469518784.txt" 6 "1260" 4 "gain" 3012291 155625629 8478629 9241084 "PPAB_ 24_1f_PT_251469518532.txt,PPAB_3_6b_PT_251469518594.txt,PPAB_4_9a_PT_2 51469518575.txt,PPAB_9_1g_PT_251469518604.txt,PPAC_4_1c_PT_25146951878 4.txt" 5
DNAcopy cghMCR DNAcopy cghMCR • 665 views
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